First off I'd want to identify exactly how the latency in question is being identified. Is it a particular application running slowly or a wide variety of traffic that can be specifically observed with either long transit times or loss?
If it is something specific to one type of application traffic and it isn't the actual application (a very common theme, unfortunately) then I'd want to understand the nature of the traffic that was slow and try to see if I could isolate it. Is it high-bandwidth / large packet that's causing the issue? Lots of small packets?
Finally, some basic isolation might shed some light - can you send the same type of traffic experiencing high latency between two hosts on the same vSwitch (i.e. exclude the physical switch)? Between hosts on two different hypervisors on the same blade switch (exclude the Nexus and its connections)?
The other common causes should also be ruled out - taking errors on any physical interfaces (in either direction), weird STP/L2 configuration problems (incredibly common on blade switch configurations, unfortunately), tell-tale error messages, counters for packet drops on anything in line, etc.